Mr. Gobler said oxygen levels in the Peconic Estuaries began dropping Wednesday night as the algae became more dense. By Friday, readings from the County Road 105 bridge showed zero oxygen in the water for the fish to breathe.

When a school of bunker swam into this “dead zone,” they suffocated and died, he said. There have been reports of thousands of the dead bunker washing up along town and private beaches.

“This is a pretty remarkable size fish kill,” Mr. Gobler noted. “There were fished piled on top of each other on the shoreline.”

Mr. Walter said that may pose a public safety hazard. While the town is working with the state Department of Environmental Conservation, Mr. Walter said they’ll need to dispose of the dead fish somehow.

Ideally, the fish would be cleaned up and moved to the Brookhaven landfill, if the DEC allows that, he said. Otherwise, Mr. Walter said he may declare a town-wide state of emergency to clean up the fish and bury them at the town’s own waste facility.

“We’re ready to take action, we just don’t know what action we’re going to take,” Mr. Walter said. “The next 24 hours will tell.”

While the town waits for DEC approval, Mr. Walter said local boat captains have been contacted to round up bunker in the Peconic Estuary before they continue to die off.

Nate Phillips, a commercial fisherman from Greenport, is one of those boat captains. Normally, fishermen are only allowed to take a certain quota of bunker, which are used by lobstermen and other fishermen as bait. Mr. Phillips said those restrictions may be voided during this crisis.

“Obviously, the ultimate goal is to get it cleaned up before they all die,” he said. “When they die they’re a terrible, stinky mess.”

Mr. Phillips told the News-Review he was rounding up a group of fishermen — as many as five or six boats — to harvest the fish using haul seines, scoop nets, or “basically whatever we can get them with.”

The harvest could begin as early as Saturday night.

Dead fish that turned up near the Riverhead Yacht Club Friday afternoon. (Credit: Melanie Drozd)

Mr. Gobler said fish kills are not unusual, but they’re not seen as often in other parts of Long Island where the bunker group together to spawn.

“There’s very few places on Long Island where oxygen levels are going to zero for multiple hours,” he said. “That’s not normal.”

Mr. Gobler said nitrogen runoff likely fed this specific algal bloom, nicknamed “mahogany tide.” Shallow creeks and tributaries of the river are especially vulnerable to algae blooms because the nitrogen gets concentrated in one area.

Historically, the Peconic Estuary has had relatively low oxygen levels to begin with, Mr. Gobler said. With these blooms moving in, the River will “probably have oxygen problems through the summer,” he said.

“It’s going to hit low and no oxygen levels throughout the summer,” he said. “But there may not be the equivalent fish kills because … the fish will sense the low oxygen levels and turn around.”